By means of two different parametrizations of quark energy loss and the nuclear parton distributions determined only with lepton-nuclear deep inelastic scattering experimental data, a leading order phenomenological analysis is performed on the nuclear Drell-Yan differential cross section ratios for E772 experimental data. Uncertainty due to the quark energy loss effect is quantified in determining the nuclear sea quark distribution by using nuclear Drell-Yan data. It is found that the quark energy loss effect on nuclear Drell-Yan cross section ratios becomes greater with the increase of quark momentum fraction in the target nuclei. The uncertainty from the quark energy loss becomes bigger as the nucleus A becomes heavier. The Drell-Yan data on proton incident middle and heavy nuclei versus deuterium would result in an overestimate for nuclear modification in the sea quark distribution with neglecting the quark energy loss.